Comparative Genomic Analysis Of Enterococcus Faecalis Isolated From Dairy Products And Other Environments

Enterococcus faecalis(E.faecalis),as an important type species of Enterococcus,is ubiquitous in nature and has been isolated from many different environments.However,there is less research in Comparative genomic analysis of E.faecalis isolated from dairy products and other environments.In this study,15 naturally fermented dairy strains sequenced by Illumina Miseq high-throughput sequencing technique and 63 genome sequences retrieved from the Genbank database.a total of 78 strains of E.faecalis were subjected to comparative genomic analysis,We believe that this comparative genomics analysis can provide the insight necessary to understand the genetic relationships between these E.faecalis strains and the adaptive mechanisms that have evolved to allow them to persist in different environments.So we analyzed the evolution of strains,environmental specific genes,drug resistance genes,virulence genes and pre-phages.and to evaluate the safety of E.faecalis in natural fermented dairy products.The results were showed as bellow:The genomes of the E.faecalis strain has a low G+C content ranging from 37.0% to 38.0%,The average genome size was 2.94 ± 0.15 Mb,with 2,884 ± 211 predicted genes.On average,the strains from water had the smallest genome size and the minimum number of predicted genes,which was significantly different from the strains from blood(P < 0.01).In addition,the strains from dairy products and blood differed significantly in the number of predicted genes(P < 0.01).There were no significant differences in the genome size or number of predicted genes among the blood-,faeces-,and urine-originated strains.The pan-genome of the 78 E.faecalis strains was composed of 10,573 gene families,and the core gene set contained 1,361 genes.Functional analysis of the representative genes in the pan-and core-genome was conducted based on the COG database.The core genes were mainly distributed in the categories representing carbohydrate transport and metabolism,nucleotide transport and metabolism and amino acid transport and metabolism;As a large proportion of genes were dispensable,pan-genome expansion happened in each functional category in varying degree compared with the core-genome,The largest extent of expansion occurred in the group of genes involving in defense mechanisms.To investigate the phylogenetic relationship between the 78 strains,with the concatenated nucleotide sequence of the core genes of each strain.The strains from the different environments were dispersed evenly among the four branches,suggesting no correlation between the isolation environment and strain phylogeny.While our in-depth analysis of the functional genomes did reveal environment-specific adaptation in E.faecalis strains originated from dairy products,water,and blood All these findings suggest that the natural environment where the strain was recovered is effective in shaping the E.faecalis genomes.A total of 88 virulence genes were identified in 76 E.faecalis strains with the virulence factor database,which were involved in the adhesion,phagocytosis and invasion of the strains.The virulence gene and phage sequence of dairy products isolates were not significantly different from those of other environmental isolates.Therefore,E.faecalis is at risk of disease in dairy products.it is suggested that the safety of E.faecalis in dairy products should be evaluated roundly.